Select the overview window menu item to get a navigable image - of the whole alignment.

The red box indicates the currently viewed region of the alignment, this may be moved by clicking and dragging with the mouse.

2.10.1
29/11/2016 diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 90f6832..297233d 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -24,15 +24,27 @@

+ Jalview 2.10.2b1 bugfix release +

+ This is patch release for 2.10.2. See the release notes for full + details bugs addressed in this version, which also introduces + additional improvements to the overview panel, and patches for + several minor issues including the ability to correctly recover + cross-references for Uniprot protein sequences from Ensembl. +

What's new in Jalview 2.10.2 ?

- This August 2017 release of Jalview introduces new user interface - features, improved and more extensible tree and PCA analysis, more - robust 3D structure viewing with UCSF Chimera and an updated service - client for JABAWS. The full list of bug fixes and new features can - be found in the 2.10.2 - Release Notes, but the highlights are below. + Version 2.10.2 was released in August 2017, and introduced new user + interface features, improved and more extensible tree and PCA + analysis, more robust 3D structure viewing with UCSF Chimera and an + updated service client for JABAWS. The full list of bug fixes and + new features can be found in the 2.10.2 Release Notes, but + the highlights are below.

New dialog and faster and more diff --git a/lib/jabaws-min-client-2.2.0.jar b/lib/jabaws-min-client-2.2.0.jar index bf1e8b1..37426c3 100644 Binary files a/lib/jabaws-min-client-2.2.0.jar and b/lib/jabaws-min-client-2.2.0.jar differ diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 162f10f..9f3ab70 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -1311,3 +1311,13 @@ label.occupancy_descr = Number of aligned positions label.show_experimental = Enable experimental features label.show_experimental_tip = Enable any new and currently 'experimental' features (see Latest Release Notes for details) label.warning_hidden = Warning: {0} {1} is currently hidden +label.overview_settings = Overview settings +label.ov_legacy_gap = Use legacy gap colouring (gaps are white) +label.gap_colour = Gap colour: +label.ov_show_hide_default = Show hidden regions when opening overview +label.hidden_colour = Hidden colour: +label.select_gap_colour = Select gap colour +label.select_hidden_colour = Select hidden colour +label.overview = Overview +label.reset_to_defaults = Reset to defaults +label.oview_calc = Recalculating overview... diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties index 8385142..1e3a391 100644 --- a/resources/lang/Messages_es.properties +++ b/resources/lang/Messages_es.properties @@ -1311,3 +1311,13 @@ label.togglehidden = Mostrar regiones ocultas label.show_experimental = Habilitar funciones experimentales label.show_experimental_tip = Habilitar funciones nuevas y experimentales (ver Latest Release Notes para más detalles) label.warning_hidden = Advertencia: {0} {1} está actualmente oculto +label.overview_settings = Ajustes para la ventana resumen +label.ov_legacy_gap = Utilizar el color heredado de huecos
(los huecos son blancos) +label.gap_colour = Color de huecos: +label.ov_show_hide_default = Mostrar regiones ocultas al abrir el resumen +label.hidden_colour = Color de las regiones ocultas: +label.select_gap_colour = Seleccionar color de huecos +label.select_hidden_colour = Seleccionar color de las regiones ocultas +label.overview = Resumen +label.reset_to_defaults = Restablecen a los predeterminados +label.oview_calc = Recalculando resumen diff --git a/src/jalview/api/AlignmentColsCollectionI.java b/src/jalview/api/AlignmentColsCollectionI.java index 3a3f660..06b1675 100644 --- a/src/jalview/api/AlignmentColsCollectionI.java +++ b/src/jalview/api/AlignmentColsCollectionI.java @@ -30,4 +30,11 @@ public interface AlignmentColsCollectionI extends Iterable * @return true if the column at the position is hidden */ public boolean isHidden(int c); + + /** + * Answers if any column in this collection is hidden + * + * @return true if there is at least 1 hidden column + */ + public boolean hasHidden(); } diff --git a/src/jalview/api/AlignmentRowsCollectionI.java b/src/jalview/api/AlignmentRowsCollectionI.java index 24affc5..fbf6ceb 100644 --- a/src/jalview/api/AlignmentRowsCollectionI.java +++ b/src/jalview/api/AlignmentRowsCollectionI.java @@ -34,6 +34,13 @@ public interface AlignmentRowsCollectionI extends Iterable public boolean isHidden(int r); /** + * Answers if any row in this collection is hidden + * + * @return true if there is at least 1 hidden row + */ + public boolean hasHidden(); + + /** * Answers the sequence at the given position in the alignment * * @param r diff --git a/src/jalview/api/RendererListenerI.java b/src/jalview/api/RendererListenerI.java new file mode 100644 index 0000000..0ce4116 --- /dev/null +++ b/src/jalview/api/RendererListenerI.java @@ -0,0 +1,28 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.api; + +import java.beans.PropertyChangeListener; + +public interface RendererListenerI extends PropertyChangeListener +{ + +} diff --git a/src/jalview/appletgui/OverviewCanvas.java b/src/jalview/appletgui/OverviewCanvas.java index a0466d3..9597b44 100644 --- a/src/jalview/appletgui/OverviewCanvas.java +++ b/src/jalview/appletgui/OverviewCanvas.java @@ -21,6 +21,7 @@ package jalview.appletgui; import jalview.renderer.OverviewRenderer; +import jalview.renderer.OverviewResColourFinder; import jalview.viewmodel.OverviewDimensions; import java.awt.Color; @@ -48,10 +49,6 @@ public class OverviewCanvas extends Component private AlignViewport av; - // Can set different properties in this seqCanvas than - // main visible SeqCanvas - private SequenceRenderer sr; - private jalview.renderer.seqfeatures.FeatureRenderer fr; private Frame nullFrame; @@ -65,10 +62,6 @@ public class OverviewCanvas extends Component nullFrame = new Frame(); nullFrame.addNotify(); - sr = new SequenceRenderer(av); - sr.graphics = nullFrame.getGraphics(); - sr.renderGaps = false; - sr.forOverview = true; fr = new jalview.renderer.seqfeatures.FeatureRenderer(av); } @@ -119,7 +112,8 @@ public class OverviewCanvas extends Component setPreferredSize(new Dimension(od.getWidth(), od.getHeight())); - or = new OverviewRenderer(sr, fr, od); + or = new OverviewRenderer(fr, od, av.getAlignment(), + av.getResidueShading(), new OverviewResColourFinder()); miniMe = nullFrame.createImage(od.getWidth(), od.getHeight()); offscreen = nullFrame.createImage(od.getWidth(), od.getHeight()); diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java index be552c0..e74e1cd 100755 --- a/src/jalview/appletgui/OverviewPanel.java +++ b/src/jalview/appletgui/OverviewPanel.java @@ -148,11 +148,12 @@ public class OverviewPanel extends Panel implements Runnable, } else { + // don't do anything if the mouse press is in the overview's box + // (wait to see if it's a drag instead) + // otherwise update the viewport if (!od.isPositionInBox(evt.getX(), evt.getY())) - { - // don't do anything if the mouse press is in the overview's box - // (wait to see if it's a drag instead) - // otherwise update the viewport + { + draggingBox = false; od.updateViewportFromMouse(evt.getX(), evt.getY(), av.getAlignment().getHiddenSequences(), av.getAlignment().getHiddenColumns()); @@ -170,10 +171,6 @@ public class OverviewPanel extends Panel implements Runnable, @Override public void mouseReleased(MouseEvent evt) { - if (draggingBox) - { - draggingBox = false; - } } @Override diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java index be4f9e6..57bfa68 100644 --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@ -1451,7 +1451,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, { if (scrollThread != null) { - scrollThread.running = false; + scrollThread.threadRunning = false; scrollThread = null; } @@ -1701,7 +1701,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, mouseExited(evt); } - if (scrollThread != null) + if ((scrollThread != null) && (scrollThread.isRunning())) { scrollThread.setEvent(evt); } @@ -1717,9 +1717,9 @@ public class SeqPanel extends Panel implements MouseMotionListener, oldSeq = 0; } - if (scrollThread != null) + if ((scrollThread != null) && (scrollThread.isRunning())) { - scrollThread.running = false; + scrollThread.stopScrolling(); scrollThread = null; } } @@ -1742,9 +1742,9 @@ public class SeqPanel extends Panel implements MouseMotionListener, { if (evt == null) { - if (scrollThread != null) + if ((scrollThread != null) && (scrollThread.isRunning())) { - scrollThread.running = false; + scrollThread.stopScrolling(); scrollThread = null; } mouseDragging = false; @@ -1767,7 +1767,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, { MouseEvent evt; - boolean running = false; + private volatile boolean threadRunning = true; public ScrollThread() { @@ -1781,14 +1781,18 @@ public class SeqPanel extends Panel implements MouseMotionListener, public void stopScrolling() { - running = false; + threadRunning = false; + } + + public boolean isRunning() + { + return threadRunning; } @Override public void run() { - running = true; - while (running) + while (threadRunning) { if (evt != null) @@ -1797,23 +1801,23 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (mouseDragging && evt.getY() < 0 && av.getRanges().getStartSeq() > 0) { - running = av.getRanges().scrollUp(true); + av.getRanges().scrollUp(true); } if (mouseDragging && evt.getY() >= getSize().height && av .getAlignment().getHeight() > av.getRanges().getEndSeq()) { - running = av.getRanges().scrollUp(false); + av.getRanges().scrollUp(false); } if (mouseDragging && evt.getX() < 0) { - running = av.getRanges().scrollRight(false); + av.getRanges().scrollRight(false); } else if (mouseDragging && evt.getX() >= getSize().width) { - running = av.getRanges().scrollRight(true); + av.getRanges().scrollRight(true); } } diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java index a382c60..e55f2a5 100755 --- a/src/jalview/appletgui/SequenceRenderer.java +++ b/src/jalview/appletgui/SequenceRenderer.java @@ -22,7 +22,7 @@ package jalview.appletgui; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; -import jalview.renderer.ResidueShaderI; +import jalview.renderer.ResidueColourFinder; import jalview.renderer.seqfeatures.FeatureColourFinder; import java.awt.Color; @@ -40,19 +40,18 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer boolean renderGaps = true; - SequenceGroup currentSequenceGroup = null; - SequenceGroup[] allGroups = null; Color resBoxColour; Graphics graphics; - boolean forOverview = false; + ResidueColourFinder resColourFinder; public SequenceRenderer(AlignViewport av) { this.av = av; + resColourFinder = new ResidueColourFinder(); } /** @@ -69,25 +68,6 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer this.renderGaps = renderGaps; } - protected Color getResidueBoxColour(SequenceI seq, int i) - { - allGroups = av.getAlignment().findAllGroups(seq); - - if (inCurrentSequenceGroup(i)) - { - if (currentSequenceGroup.getDisplayBoxes()) - { - getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, i); - } - } - else if (av.getShowBoxes()) - { - getBoxColour(av.getResidueShading(), seq, i); - } - - return resBoxColour; - } - /** * Get the residue colour at the given sequence position - as determined by * the sequence group colour (if any), else the colour scheme, possibly @@ -104,31 +84,9 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer { // TODO replace 8 or so code duplications with calls to this method // (refactored as needed) - Color col = getResidueBoxColour(seq, position); - - if (finder != null) - { - col = finder.findFeatureColour(col, seq, position); - } - return col; - } - - void getBoxColour(ResidueShaderI shader, SequenceI seq, int i) - { - if (shader.getColourScheme() != null) - { - resBoxColour = shader.findColour(seq.getCharAt(i), i, seq); - } - else if (forOverview - && !jalview.util.Comparison.isGap(seq.getCharAt(i))) - { - resBoxColour = Color.lightGray; - } - else - { - resBoxColour = Color.white; - } - + return resColourFinder.getResidueColour(av.getShowBoxes(), + av.getResidueShading(), + allGroups, seq, position, finder); } public Color findSequenceColour(SequenceI seq, int i) @@ -165,23 +123,28 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer int curWidth = av.getCharWidth(), avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight(); + Color resBoxColour = Color.white; Color tempColour = null; while (i <= end) { resBoxColour = Color.white; if (i < length) { - if (inCurrentSequenceGroup(i)) + SequenceGroup currentSequenceGroup = resColourFinder + .getCurrentSequenceGroup(allGroups, i); + if (currentSequenceGroup != null) { if (currentSequenceGroup.getDisplayBoxes()) { - getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, + resBoxColour = resColourFinder.getBoxColour( + currentSequenceGroup.getGroupColourScheme(), seq, i); } } else if (av.getShowBoxes()) { - getBoxColour(av.getResidueShading(), seq, i); + resBoxColour = resColourFinder + .getBoxColour(av.getResidueShading(), seq, i); } } @@ -245,7 +208,9 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer continue; } - if (inCurrentSequenceGroup(i)) + SequenceGroup currentSequenceGroup = resColourFinder + .getCurrentSequenceGroup(allGroups, i); + if (currentSequenceGroup != null) { if (!currentSequenceGroup.getDisplayText()) { @@ -254,7 +219,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer if (currentSequenceGroup.getColourText()) { - getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, i); + resBoxColour = resColourFinder.getBoxColour( + currentSequenceGroup.getGroupColourScheme(), seq, i); graphics.setColor(resBoxColour.darker()); } if (currentSequenceGroup.getShowNonconserved()) @@ -271,7 +237,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer if (av.getColourText()) { - getBoxColour(av.getResidueShading(), seq, i); + resBoxColour = resColourFinder + .getBoxColour(av.getResidueShading(), seq, i); if (av.getShowBoxes()) { graphics.setColor(resBoxColour.darker()); @@ -358,28 +325,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer return sequenceChar; } - boolean inCurrentSequenceGroup(int res) - { - if (allGroups == null) - { - return false; - } - - for (int i = 0; i < allGroups.length; i++) - { - if (allGroups[i].getStartRes() <= res - && allGroups[i].getEndRes() >= res) - { - currentSequenceGroup = allGroups[i]; - return true; - } - } - - return false; - } - - public void drawHighlightedText(SequenceI seq, int start, int end, int x1, - int y1) + public void drawHighlightedText(SequenceI seq, int start, int end, + int x1, int y1) { int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight(); int pady = avCharHeight / 5; diff --git a/src/jalview/commands/RemoveGapColCommand.java b/src/jalview/commands/RemoveGapColCommand.java index 3266874..32e5fb4 100644 --- a/src/jalview/commands/RemoveGapColCommand.java +++ b/src/jalview/commands/RemoveGapColCommand.java @@ -20,25 +20,6 @@ */ package jalview.commands; -/* - * Jalview - A Sequence Alignment Editor and Viewer Copyright (C) 2007 AM - * Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or modify it under - * the terms of the GNU General Public License as published by the Free Software - * Foundation; either version 2 of the License, or (at your option) any later - * version. - * - * This program is distributed in the hope that it will be useful, but WITHOUT - * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS - * FOR A PARTICULAR PURPOSE. See the GNU General Public License for more - * details. - * - * You should have received a copy of the GNU General Public License along with - * this program; if not, write to the Free Software Foundation, Inc., 51 - * Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ - import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; @@ -110,6 +91,7 @@ public class RemoveGapColCommand extends EditCommand performEdit(0, null); } + @Override public int getSize() { // We're interested in the number of columns deleted, diff --git a/src/jalview/commands/RemoveGapsCommand.java b/src/jalview/commands/RemoveGapsCommand.java index c5c35f1..27831dd 100644 --- a/src/jalview/commands/RemoveGapsCommand.java +++ b/src/jalview/commands/RemoveGapsCommand.java @@ -20,25 +20,6 @@ */ package jalview.commands; -/* - * Jalview - A Sequence Alignment Editor and Viewer Copyright (C) 2007 AM - * Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or modify it under - * the terms of the GNU General Public License as published by the Free Software - * Foundation; either version 2 of the License, or (at your option) any later - * version. - * - * This program is distributed in the hope that it will be useful, but WITHOUT - * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS - * FOR A PARTICULAR PURPOSE. See the GNU General Public License for more - * details. - * - * You should have received a copy of the GNU General Public License along with - * this program; if not, write to the Free Software Foundation, Inc., 51 - * Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ - import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java index 1b5207f..084b80e 100755 --- a/src/jalview/datamodel/AlignmentI.java +++ b/src/jalview/datamodel/AlignmentI.java @@ -5,16 +5,16 @@ * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General License + * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General License for more details. + * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General License + * You should have received a copy of the GNU General Public License * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ diff --git a/src/jalview/datamodel/AllColsCollection.java b/src/jalview/datamodel/AllColsCollection.java index 4ac4f83..e216c46 100644 --- a/src/jalview/datamodel/AllColsCollection.java +++ b/src/jalview/datamodel/AllColsCollection.java @@ -50,4 +50,10 @@ public class AllColsCollection implements AlignmentColsCollectionI { return !hidden.isVisible(c); } + + @Override + public boolean hasHidden() + { + return hidden.hasHiddenColumns(); + } } diff --git a/src/jalview/datamodel/AllRowsCollection.java b/src/jalview/datamodel/AllRowsCollection.java index 9a33094..10c47f0 100644 --- a/src/jalview/datamodel/AllRowsCollection.java +++ b/src/jalview/datamodel/AllRowsCollection.java @@ -59,4 +59,10 @@ public class AllRowsCollection implements AlignmentRowsCollectionI { return alignment.getSequenceAtAbsoluteIndex(seq); } + + @Override + public boolean hasHidden() + { + return (hidden.getSize() > 0); + } } diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index 6964b53..e2f15e1 100755 --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@ -27,6 +27,8 @@ import jalview.renderer.ResidueShaderI; import jalview.schemes.ColourSchemeI; import java.awt.Color; +import java.beans.PropertyChangeListener; +import java.beans.PropertyChangeSupport; import java.util.ArrayList; import java.util.List; import java.util.Map; @@ -39,6 +41,26 @@ import java.util.Map; */ public class SequenceGroup implements AnnotatedCollectionI { + // TODO ideally this event notification functionality should be separated into + // a + // subclass of ViewportProperties similarly to ViewportRanges. Done here as + // quick fix for JAL-2665 + public static final String SEQ_GROUP_CHANGED = "Sequence group changed"; + + protected PropertyChangeSupport changeSupport = new PropertyChangeSupport( + this); + + public void addPropertyChangeListener(PropertyChangeListener listener) + { + changeSupport.addPropertyChangeListener(listener); + } + + public void removePropertyChangeListener(PropertyChangeListener listener) + { + changeSupport.removePropertyChangeListener(listener); + } + // end of event notification functionality initialisation + String groupName; String description; @@ -496,6 +518,8 @@ public class SequenceGroup implements AnnotatedCollectionI if (s != null && !sequences.contains(s)) { sequences.add(s); + changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, + sequences.size() - 1, sequences.size()); } if (recalc) @@ -693,6 +717,8 @@ public class SequenceGroup implements AnnotatedCollectionI synchronized (sequences) { sequences.remove(s); + changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, + sequences.size() + 1, sequences.size()); if (recalc) { @@ -729,7 +755,9 @@ public class SequenceGroup implements AnnotatedCollectionI */ public void setStartRes(int i) { + int before = startRes; startRes = i; + changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes); } /** @@ -739,7 +767,9 @@ public class SequenceGroup implements AnnotatedCollectionI */ public void setEndRes(int i) { + int before = endRes; endRes = i; + changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, endRes); } /** @@ -1349,7 +1379,10 @@ public class SequenceGroup implements AnnotatedCollectionI { synchronized (sequences) { + int before = sequences.size(); sequences.clear(); + changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, + sequences.size()); } } diff --git a/src/jalview/datamodel/VisibleColsCollection.java b/src/jalview/datamodel/VisibleColsCollection.java index bc32fac..e9437a7 100644 --- a/src/jalview/datamodel/VisibleColsCollection.java +++ b/src/jalview/datamodel/VisibleColsCollection.java @@ -51,4 +51,10 @@ public class VisibleColsCollection implements AlignmentColsCollectionI return false; } + @Override + public boolean hasHidden() + { + return false; + } + } diff --git a/src/jalview/datamodel/VisibleRowsCollection.java b/src/jalview/datamodel/VisibleRowsCollection.java index ee0557f..fd7cf47 100644 --- a/src/jalview/datamodel/VisibleRowsCollection.java +++ b/src/jalview/datamodel/VisibleRowsCollection.java @@ -56,4 +56,10 @@ public class VisibleRowsCollection implements AlignmentRowsCollectionI { return alignment.getSequenceAtAbsoluteIndex(seq); } + + @Override + public boolean hasHidden() + { + return false; + } } diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java index fe3f6ef..2de100b 100644 --- a/src/jalview/datamodel/xdb/embl/EmblEntry.java +++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java @@ -279,7 +279,7 @@ public class EmblEntry String translation = null; String proteinName = ""; String proteinId = null; - Map vals = new Hashtable(); + Map vals = new Hashtable<>(); /* * codon_start 1/2/3 in EMBL corresponds to phase 0/1/2 in CDS diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 922e481..fe216c0 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1103,8 +1103,8 @@ public class AlignmentPanel extends GAlignmentPanel implements * single graphics context), then reset to (0, scale height) */ alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight); - getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes, - startSeq, endSeq, 0); + getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes, + endRes, startSeq, endSeq); alignmentGraphics.translate(-alignmentGraphicsOffset, 0); if (av.isShowAnnotation() && (endSeq == alignmentHeight)) @@ -1231,7 +1231,7 @@ public class AlignmentPanel extends GAlignmentPanel implements pg.translate(idWidth, 0); - getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, + getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(pg, pwidth - idWidth, totalHeight, 0); if ((pi * pheight) < totalHeight) diff --git a/src/jalview/gui/FontChooser.java b/src/jalview/gui/FontChooser.java index 5271e4f..6cddcca 100755 --- a/src/jalview/gui/FontChooser.java +++ b/src/jalview/gui/FontChooser.java @@ -327,22 +327,17 @@ public class FontChooser extends GFontChooser ap.fontChanged(); /* - * adjust other half of split frame if any, if either same - * font, or proportionate scaling, is selected + * adjust other half of split frame if present, whether or not same font or + * scale to cDNA is selected, because a font change may affect character + * width, and this is kept the same in both panels */ - if (fontAsCdna.isEnabled()) + if (fontAsCdna.isVisible()) { if (fontAsCdna.isSelected()) { - /* - * copy the font - */ ap.av.getCodingComplement().setFont(newFont, true); } - /* - * adjust layout for font change / reset / sizing - */ SplitFrame splitFrame = (SplitFrame) ap.alignFrame .getSplitViewContainer(); splitFrame.adjustLayout(); diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java index 27f9c3f..64bf15c 100644 --- a/src/jalview/gui/OverviewCanvas.java +++ b/src/jalview/gui/OverviewCanvas.java @@ -21,18 +21,29 @@ package jalview.gui; import jalview.api.AlignViewportI; +import jalview.bin.Cache; import jalview.renderer.OverviewRenderer; +import jalview.renderer.OverviewResColourFinder; import jalview.viewmodel.OverviewDimensions; +import java.awt.AlphaComposite; import java.awt.Color; import java.awt.Dimension; import java.awt.Graphics; +import java.awt.Graphics2D; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; import java.awt.image.BufferedImage; import javax.swing.JComponent; +import javax.swing.Timer; public class OverviewCanvas extends JComponent { + private static final long RUNNING_TIME = 1000; + + private static final int SPEED = 40; + private static final Color TRANS_GREY = new Color(100, 100, 100, 25); // This is set true if the alignment view changes whilst @@ -41,10 +52,14 @@ public class OverviewCanvas extends JComponent private volatile boolean updaterunning = false; + private boolean dispose = false; + private BufferedImage miniMe; private BufferedImage lastMiniMe = null; + private BufferedImage veryLastMiniMe = null; + // Can set different properties in this seqCanvas than // main visible SeqCanvas private SequenceRenderer sr; @@ -57,16 +72,67 @@ public class OverviewCanvas extends JComponent private AlignViewportI av; + + private OverviewResColourFinder cf; + + private float alpha = 0f; + + private long startTime = -1; + + private final Timer timer; + + private ProgressPanel progressPanel; + public OverviewCanvas(OverviewDimensions overviewDims, - AlignViewportI alignvp) + AlignViewportI alignvp, ProgressPanel pp) { od = overviewDims; av = alignvp; + progressPanel = pp; sr = new SequenceRenderer(av); sr.renderGaps = false; - sr.forOverview = true; fr = new jalview.renderer.seqfeatures.FeatureRenderer(av); + + boolean useLegacy = Cache.getDefault(Preferences.USE_LEGACY_GAP, false); + Color gapCol = Cache.getDefaultColour(Preferences.GAP_COLOUR, + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP); + Color hiddenCol = Cache.getDefaultColour(Preferences.HIDDEN_COLOUR, + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN); + cf = new OverviewResColourFinder(useLegacy, gapCol, hiddenCol); + + setSize(od.getWidth(), od.getHeight()); + + timer = new Timer(SPEED, new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + if (startTime < 0) + { + startTime = System.currentTimeMillis(); + } + else + { + + long time = System.currentTimeMillis(); + long duration = time - startTime; + if (duration >= RUNNING_TIME) + { + startTime = -1; + ((Timer) e.getSource()).stop(); + alpha = 0f; + } + else + { + alpha = 1f - ((float) duration / (float) RUNNING_TIME); + } + repaint(); + } + } + }); + } /** @@ -118,6 +184,7 @@ public class OverviewCanvas extends JComponent FeatureRenderer transferRenderer) { miniMe = null; + veryLastMiniMe = lastMiniMe; if (showSequenceFeatures) { @@ -126,7 +193,11 @@ public class OverviewCanvas extends JComponent setPreferredSize(new Dimension(od.getWidth(), od.getHeight())); - or = new OverviewRenderer(sr, fr, od); + or = new OverviewRenderer(fr, od, av.getAlignment(), + av.getResidueShading(), cf); + + or.addPropertyChangeListener(progressPanel); + miniMe = or.draw(od.getRows(av.getAlignment()), od.getColumns(av.getAlignment())); @@ -142,15 +213,22 @@ public class OverviewCanvas extends JComponent } System.gc(); + or.removePropertyChangeListener(progressPanel); + or = null; if (restart) { restart = false; - draw(showSequenceFeatures, showAnnotation, transferRenderer); + if (!dispose) + { + draw(showSequenceFeatures, showAnnotation, transferRenderer); + } } else { updaterunning = false; lastMiniMe = miniMe; + alpha = 1f; + timer.start(); } } @@ -173,16 +251,88 @@ public class OverviewCanvas extends JComponent } else if (lastMiniMe != null) { - g.drawImage(lastMiniMe, 0, 0, this); - if (lastMiniMe != miniMe) + // is this a resize? + if ((getWidth() > 0) && (getHeight() > 0) + && ((getWidth() != od.getWidth()) + || (getHeight() != od.getHeight()))) { - g.setColor(TRANS_GREY); - g.fillRect(0, 0, getWidth(), getHeight()); + // if there is annotation, scale the alignment and annotation separately + if (od.getGraphHeight() > 0) + { + BufferedImage topImage = lastMiniMe.getSubimage(0, 0, + od.getWidth(), od.getSequencesHeight()); + BufferedImage bottomImage = lastMiniMe.getSubimage(0, + od.getSequencesHeight(), od.getWidth(), + od.getGraphHeight()); + + // must be done at this point as we rely on using old width/height + // above, and new width/height below + od.setWidth(getWidth()); + od.setHeight(getHeight()); + + // stick the images back together so lastMiniMe is consistent in the + // event of a repaint - BUT probably not thread safe + lastMiniMe = new BufferedImage(od.getWidth(), od.getHeight(), + BufferedImage.TYPE_INT_RGB); + Graphics lg = lastMiniMe.getGraphics(); + lg.drawImage(topImage, 0, 0, od.getWidth(), + od.getSequencesHeight(), null); + lg.drawImage(bottomImage, 0, od.getSequencesHeight(), + od.getWidth(), od.getGraphHeight(), this); + lg.dispose(); + } + else + { + od.setWidth(getWidth()); + od.setHeight(getHeight()); + } + + // scale lastMiniMe to the new size + g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this); + + // make sure the box is in the right place + od.setBoxPosition(av.getAlignment().getHiddenSequences(), + av.getAlignment().getHiddenColumns()); + } + else // not a resize + { + if (alpha != 0) // this is a timer triggered dissolve + { + Graphics2D g2d = (Graphics2D) g.create(); + + // draw the original image + g2d.drawImage(veryLastMiniMe, 0, 0, getWidth(), getHeight(), + this); + + // draw the new image on top with varying degrees of transparency + g2d.setComposite(AlphaComposite.SrcOver.derive(1f - alpha)); + g2d.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this); + + g2d.dispose(); + } + else + { + // fall back to normal behaviour + g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this); + } } } + // draw the box g.setColor(Color.red); od.drawBox(g); } + public void dispose() + { + dispose = true; + synchronized (this) + { + restart = true; + if (or != null) + { + or.setRedraw(true); + } + } + } } diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java index 28de801..51d7a84 100755 --- a/src/jalview/gui/OverviewPanel.java +++ b/src/jalview/gui/OverviewPanel.java @@ -20,6 +20,8 @@ */ package jalview.gui; +import jalview.bin.Cache; +import jalview.renderer.OverviewRenderer; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.viewmodel.OverviewDimensions; @@ -68,6 +70,8 @@ public class OverviewPanel extends JPanel private boolean draggingBox = false; + private ProgressPanel progressPanel; + /** * Creates a new OverviewPanel object. * @@ -79,30 +83,62 @@ public class OverviewPanel extends JPanel this.av = alPanel.av; this.ap = alPanel; - od = new OverviewDimensionsShowHidden(av.getRanges(), + showHidden = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, + true); + if (showHidden) + { + od = new OverviewDimensionsShowHidden(av.getRanges(), (av.isShowAnnotation() && av.getAlignmentConservationAnnotation() != null)); + } + else + { + od = new OverviewDimensionsHideHidden(av.getRanges(), + (av.isShowAnnotation() + && av.getAlignmentConservationAnnotation() != null)); + } - setSize(od.getWidth(), od.getHeight()); - - oviewCanvas = new OverviewCanvas(od, av); setLayout(new BorderLayout()); + progressPanel = new ProgressPanel(OverviewRenderer.UPDATE, + MessageManager.getString("label.oview_calc"), getWidth()); + this.add(progressPanel, BorderLayout.SOUTH); + oviewCanvas = new OverviewCanvas(od, av, progressPanel); + add(oviewCanvas, BorderLayout.CENTER); av.getRanges().addPropertyChangeListener(this); + // without this the overview window does not size to fit the overview canvas + setPreferredSize(new Dimension(od.getWidth(), od.getHeight())); + addComponentListener(new ComponentAdapter() { @Override public void componentResized(ComponentEvent evt) { - if ((getWidth() != od.getWidth()) - || (getHeight() != (od.getHeight()))) + // Resize is called on the initial display of the overview. + // This code adjusts sizes to account for the progress bar if it has not + // already been accounted for, which triggers another resize call for + // the correct sizing, at which point the overview image is updated. + // (This avoids a double recalculation of the image.) + if (getWidth() == od.getWidth() && getHeight() == od.getHeight() + + progressPanel.getHeight()) { updateOverviewImage(); - setBoxPosition(); + } + else + { + if ((getWidth() > 0) && (getHeight() > 0)) + { + od.setWidth(getWidth()); + od.setHeight(getHeight() - progressPanel.getHeight()); + } + + setPreferredSize(new Dimension(od.getWidth(), + od.getHeight() + progressPanel.getHeight())); } } + }); addMouseMotionListener(new MouseMotionAdapter() @@ -158,13 +194,13 @@ public class OverviewPanel extends JPanel } } else - // if (!av.getWrapAlignment()) { + // don't do anything if the mouse press is in the overview's box + // (wait to see if it's a drag instead) + // otherwise update the viewport if (!od.isPositionInBox(evt.getX(), evt.getY())) { - // don't do anything if the mouse press is in the overview's box - // (wait to see if it's a drag instead) - // otherwise update the viewport + draggingBox = false; od.updateViewportFromMouse(evt.getX(), evt.getY(), av.getAlignment().getHiddenSequences(), av.getAlignment().getHiddenColumns()); @@ -180,15 +216,6 @@ public class OverviewPanel extends JPanel } @Override - public void mouseReleased(MouseEvent evt) - { - if (draggingBox) - { - draggingBox = false; - } - } - - @Override public void mouseClicked(MouseEvent evt) { if (SwingUtilities.isRightMouseButton(evt)) @@ -197,8 +224,6 @@ public class OverviewPanel extends JPanel } } }); - - updateOverviewImage(); } /* @@ -266,10 +291,11 @@ public class OverviewPanel extends JPanel if ((getWidth() > 0) && (getHeight() > 0)) { od.setWidth(getWidth()); - od.setHeight(getHeight()); + od.setHeight(getHeight() - progressPanel.getHeight()); } - - setPreferredSize(new Dimension(od.getWidth(), od.getHeight())); + + setPreferredSize(new Dimension(od.getWidth(), + od.getHeight() + progressPanel.getHeight())); if (oviewCanvas.restartDraw()) { @@ -279,16 +305,21 @@ public class OverviewPanel extends JPanel Thread thread = new Thread(this); thread.start(); repaint(); + + } @Override public void run() { - oviewCanvas.draw(av.isShowSequenceFeatures(), - (av.isShowAnnotation() - && av.getAlignmentConservationAnnotation() != null), - ap.getSeqPanel().seqCanvas.getFeatureRenderer()); - setBoxPosition(); + if (oviewCanvas != null) + { + oviewCanvas.draw(av.isShowSequenceFeatures(), + (av.isShowAnnotation() + && av.getAlignmentConservationAnnotation() != null), + ap.getSeqPanel().seqCanvas.getFeatureRenderer()); + setBoxPosition(); + } } /** @@ -298,9 +329,12 @@ public class OverviewPanel extends JPanel */ private void setBoxPosition() { - od.setBoxPosition(av.getAlignment().getHiddenSequences(), - av.getAlignment().getHiddenColumns()); - repaint(); + if (od != null) + { + od.setBoxPosition(av.getAlignment().getHiddenSequences(), + av.getAlignment().getHiddenColumns()); + repaint(); + } } @Override @@ -317,8 +351,10 @@ public class OverviewPanel extends JPanel try { av.getRanges().removePropertyChangeListener(this); + oviewCanvas.dispose(); } finally { + progressPanel = null; av = null; oviewCanvas = null; ap = null; diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 3e2eba9..2ef71cc 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -455,8 +455,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener buildGroupURLMenu(sg, groupLinks); } // Add a 'show all structures' for the current selection - Hashtable pdbe = new Hashtable(), - reppdb = new Hashtable(); + Hashtable pdbe = new Hashtable<>(), reppdb = new Hashtable<>(); + SequenceI sqass = null; for (SequenceI sq : ap.av.getSequenceSelection()) { @@ -523,7 +523,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener void addFeatureLinks(final SequenceI seq, List links) { JMenu linkMenu = new JMenu(MessageManager.getString("action.link")); - Map> linkset = new LinkedHashMap>(); + Map> linkset = new LinkedHashMap<>(); for (String link : links) { @@ -609,8 +609,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener * the insertion order, which is the order of the annotations on the * alignment. */ - Map>> shownTypes = new LinkedHashMap>>(); - Map>> hiddenTypes = new LinkedHashMap>>(); + Map>> shownTypes = new LinkedHashMap<>(); + Map>> hiddenTypes = new LinkedHashMap<>(); AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes, AlignmentAnnotationUtils.asList(annotations), forSequences); @@ -716,7 +716,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener SequenceI[] seqs = ap.av.getSelectionAsNewSequence(); String[][] idandseqs = GroupUrlLink.formStrings(seqs); - Hashtable commonDbrefs = new Hashtable(); + Hashtable commonDbrefs = new Hashtable<>(); for (int sq = 0; sq < seqs.length; sq++) { @@ -1377,8 +1377,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener * Temporary store to hold distinct calcId / type pairs for the tooltip. * Using TreeMap means calcIds are shown in alphabetical order. */ - SortedMap tipEntries = new TreeMap(); - final Map> candidates = new LinkedHashMap>(); + SortedMap tipEntries = new TreeMap<>(); + final Map> candidates = new LinkedHashMap<>(); AlignmentI al = this.ap.av.getAlignment(); AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries, candidates, al); @@ -1561,7 +1561,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener void refresh() { ap.updateAnnotation(); - ap.paintAlignment(true); + // removed paintAlignment(true) here: + // updateAnnotation calls paintAlignment already, so don't need to call + // again PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); } @@ -1929,8 +1931,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener return; } - List seqs = new ArrayList(); - List features = new ArrayList(); + List seqs = new ArrayList<>(); + List features = new ArrayList<>(); /* * assemble dataset sequences, and template new sequence features, diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index c3c9239..6635dbe 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -109,6 +109,14 @@ public class Preferences extends GPreferences public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY"; + public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START"; + + public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP"; + + public static final String GAP_COLOUR = "GAP_COLOUR"; + + public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR"; + private static final int MIN_FONT_SIZE = 1; private static final int MAX_FONT_SIZE = 30; @@ -155,7 +163,7 @@ public class Preferences extends GPreferences * .properties file as '|' separated strings */ - groupURLLinks = new ArrayList(); + groupURLLinks = new ArrayList<>(); } JInternalFrame frame; @@ -309,6 +317,21 @@ public class Preferences extends GPreferences Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red)); /* + * Set overview panel defaults + */ + gapColour.setBackground( + Cache.getDefaultColour(GAP_COLOUR, + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP)); + hiddenColour.setBackground( + Cache.getDefaultColour(HIDDEN_COLOUR, + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN)); + useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false)); + gapLabel.setEnabled(!useLegacyGap.isSelected()); + gapColour.setEnabled(!useLegacyGap.isSelected()); + showHiddenAtStart + .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true)); + + /* * Set Structure tab defaults. */ final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false); @@ -631,6 +654,16 @@ public class Preferences extends GPreferences maxColour.getBackground()); /* + * Save Overview settings + */ + Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground()); + Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground()); + Cache.applicationProperties.setProperty(USE_LEGACY_GAP, + Boolean.toString(useLegacyGap.isSelected())); + Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START, + Boolean.toString(showHiddenAtStart.isSelected())); + + /* * Save Structure settings */ Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN, @@ -1035,6 +1068,63 @@ public class Preferences extends GPreferences } @Override + public void gapColour_actionPerformed(JPanel gap) + { + if (!useLegacyGap.isSelected()) + { + Color col = JColorChooser.showDialog(this, + MessageManager.getString("label.select_gap_colour"), + gapColour.getBackground()); + if (col != null) + { + gap.setBackground(col); + } + gap.repaint(); + } + } + + @Override + public void hiddenColour_actionPerformed(JPanel hidden) + { + Color col = JColorChooser.showDialog(this, + MessageManager.getString("label.select_hidden_colour"), + hiddenColour.getBackground()); + if (col != null) + { + hidden.setBackground(col); + } + hidden.repaint(); + } + + @Override + protected void useLegacyGaps_actionPerformed(ActionEvent e) + { + boolean enabled = useLegacyGap.isSelected(); + if (enabled) + { + gapColour.setBackground( + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP); + } + else + { + gapColour.setBackground( + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP); + } + gapColour.setEnabled(!enabled); + gapLabel.setEnabled(!enabled); + } + + @Override + protected void resetOvDefaults_actionPerformed(ActionEvent e) + { + useLegacyGap.setSelected(false); + useLegacyGaps_actionPerformed(null); + showHiddenAtStart.setSelected(true); + hiddenColour.setBackground( + jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN); + } + + @Override protected void userIdWidth_actionPerformed() { try diff --git a/src/jalview/gui/ProgressPanel.java b/src/jalview/gui/ProgressPanel.java new file mode 100644 index 0000000..170e9eb --- /dev/null +++ b/src/jalview/gui/ProgressPanel.java @@ -0,0 +1,148 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.gui; + +import jalview.api.RendererListenerI; + +import java.awt.BorderLayout; +import java.awt.CardLayout; +import java.awt.Color; +import java.awt.Dimension; +import java.beans.PropertyChangeEvent; + +import javax.swing.BorderFactory; +import javax.swing.JLabel; +import javax.swing.JPanel; +import javax.swing.JProgressBar; +import javax.swing.border.EmptyBorder; + +/** + * A class to manage a panel containing a label and progress bar updated by an + * event firing + * + * @author kmourao + * + */ +public class ProgressPanel extends JPanel implements RendererListenerI +{ + // max value of progress bar: values expected to be %s + private final int MAXVALUE = 100; + + private final String VISIBLE = "VISIBLE"; + + private final String INVISIBLE = "INVISIBLE"; + + // name of event property which updates the progress bar + private String eventName; + + private JProgressBar progressBar; + + private JLabel progressLabel; + + private JPanel labelPanel = new JPanel(); + + private CardLayout labelLayout = new CardLayout(); + + private JPanel barPanel = new JPanel(); + + private CardLayout barLayout = new CardLayout(); + + /** + * Construct a JPanel containing a progress bar and a label. + * + * @param eventPropertyName + * The name of the event property to update the progress bar + * @param label + * The label to place next to the progress bar + */ + public ProgressPanel(String eventPropertyName, String label, int maxwidth) + { + super(new BorderLayout(10, 0)); + setBorder(new EmptyBorder(0, 3, 0, 0)); + + eventName = eventPropertyName; + String labelText = label; + + final int w = maxwidth; + + progressBar = new JProgressBar() + { + @Override + public Dimension getMaximumSize() + { + return new Dimension(w, 1); + } + }; + progressBar.setMinimum(0); + progressBar.setPreferredSize(progressBar.getMaximumSize()); + progressLabel = new JLabel(labelText); + progressLabel.setFont(new java.awt.Font("Verdana", 0, 11)); + + // Use a CardLayout to stop the progress bar panel moving around when + // changing visibility + labelPanel.setLayout(labelLayout); + barPanel.setLayout(barLayout); + + labelPanel.add(progressLabel, VISIBLE); + labelPanel.add(new JPanel(), INVISIBLE); + barPanel.add(progressBar, VISIBLE); + barPanel.add(new JPanel(), INVISIBLE); + + labelLayout.show(labelPanel, VISIBLE); + barLayout.show(barPanel, VISIBLE); + + add(labelPanel, BorderLayout.WEST); + add(barPanel, BorderLayout.CENTER); + add(new JLabel(" "), BorderLayout.EAST); + + setBorder(BorderFactory.createLineBorder(Color.black)); + // setBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED)); + } + + @Override + /** + * Update the progress bar in response to the event. Expects the value + * supplied by the event to be in the range 0-100 i.e. a percentage + */ + public void propertyChange(PropertyChangeEvent evt) + { + if (evt.getPropertyName().equals(eventName)) + { + int progress = (int) evt.getNewValue(); + progressBar.setValue(progress); + + // switch progress bar to visible if it is not visible and current + // progress is less than MAXVALUE + // switch progress bar to invisible if it is visible and we reached + // MAXVALUE + if (progress < MAXVALUE && !progressBar.isVisible()) + { + labelLayout.show(labelPanel, VISIBLE); + barLayout.show(barPanel, VISIBLE); + } + if (progress >= MAXVALUE) + { + labelLayout.show(labelPanel, INVISIBLE); + barLayout.show(barPanel, INVISIBLE); + } + } + } +} diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index a052ae3..3d8b8aa 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -30,6 +30,7 @@ import jalview.renderer.ScaleRenderer.ScaleMark; import jalview.viewmodel.ViewportListenerI; import jalview.viewmodel.ViewportRanges; +import java.awt.AlphaComposite; import java.awt.BasicStroke; import java.awt.BorderLayout; import java.awt.Color; @@ -54,16 +55,12 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { final FeatureRenderer fr; - final SequenceRenderer sr; + final SequenceRenderer seqRdr; BufferedImage img; Graphics2D gg; - int imgWidth; - - int imgHeight; - AlignViewport av; boolean fastPaint = false; @@ -76,6 +73,14 @@ public class SeqCanvas extends JComponent implements ViewportListenerI int cursorY = 0; + int charHeight = 0; + + int charWidth = 0; + + boolean fastpainting = false; + + AnnotationPanel annotations; + /** * Creates a new SeqCanvas object. * @@ -87,7 +92,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI this.av = ap.av; updateViewport(); fr = new FeatureRenderer(ap); - sr = new SequenceRenderer(av); + seqRdr = new SequenceRenderer(av); setLayout(new BorderLayout()); PaintRefresher.Register(this, av.getSequenceSetId()); setBackground(Color.white); @@ -97,7 +102,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI public SequenceRenderer getSequenceRenderer() { - return sr; + return seqRdr; } public FeatureRenderer getFeatureRenderer() @@ -105,8 +110,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI return fr; } - int charHeight = 0, charWidth = 0; - private void updateViewport() { charHeight = av.getCharHeight(); @@ -266,7 +269,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } } - boolean fastpainting = false; /** * need to make this thread safe move alignment rendering in response to @@ -295,8 +297,9 @@ public class SeqCanvas extends JComponent implements ViewportListenerI int transX = 0; int transY = 0; - gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth, - imgHeight, -horizontal * charWidth, -vertical * charHeight); + gg.copyArea(horizontal * charWidth, vertical * charHeight, + img.getWidth(), img.getHeight(), -horizontal * charWidth, + -vertical * charHeight); if (horizontal > 0) // scrollbar pulled right, image to the left { @@ -317,7 +320,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } else { - transY = imgHeight - ((vertical + 1) * charHeight); + transY = img.getHeight() - ((vertical + 1) * charHeight); } } else if (vertical < 0) @@ -351,73 +354,201 @@ public class SeqCanvas extends JComponent implements ViewportListenerI @Override public void paintComponent(Graphics g) { - updateViewport(); - BufferedImage lcimg = img; // take reference since other threads may null - // img and call later. super.paintComponent(g); - if (lcimg != null && (fastPaint + updateViewport(); + + ViewportRanges ranges = av.getRanges(); + + int width = getWidth(); + int height = getHeight(); + + width -= (width % charWidth); + height -= (height % charHeight); + + // selectImage is the selection group outline image + BufferedImage selectImage = drawSelectionGroup( + ranges.getStartRes(), ranges.getEndRes(), + ranges.getStartSeq(), ranges.getEndSeq()); + + if ((img != null) && (fastPaint || (getVisibleRect().width != g.getClipBounds().width) || (getVisibleRect().height != g.getClipBounds().height))) { + BufferedImage lcimg = buildLocalImage(selectImage); g.drawImage(lcimg, 0, 0, this); fastPaint = false; - return; } + else if ((width > 0) && (height > 0)) + { + // img is a cached version of the last view we drew, if any + // if we have no img or the size has changed, make a new one + if (img == null || width != img.getWidth() + || height != img.getHeight()) + { + img = setupImage(); + if (img == null) + { + return; + } + gg = (Graphics2D) img.getGraphics(); + gg.setFont(av.getFont()); + } - // this draws the whole of the alignment - imgWidth = getWidth(); - imgHeight = getHeight(); + if (av.antiAlias) + { + gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); + } - imgWidth -= (imgWidth % charWidth); - imgHeight -= (imgHeight % charHeight); + gg.setColor(Color.white); + gg.fillRect(0, 0, img.getWidth(), img.getHeight()); - if ((imgWidth < 1) || (imgHeight < 1)) - { - return; + if (av.getWrapAlignment()) + { + drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes()); + } + else + { + drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(), + ranges.getStartSeq(), ranges.getEndSeq(), 0); + } + + // lcimg is a local *copy* of img which we'll draw selectImage on top of + BufferedImage lcimg = buildLocalImage(selectImage); + g.drawImage(lcimg, 0, 0, this); } + } + + /** + * Draw an alignment panel for printing + * + * @param g1 + * Graphics object to draw with + * @param startRes + * start residue of print area + * @param endRes + * end residue of print area + * @param startSeq + * start sequence of print area + * @param endSeq + * end sequence of print area + */ + public void drawPanelForPrinting(Graphics g1, int startRes, int endRes, + int startSeq, int endSeq) + { + BufferedImage selectImage = drawSelectionGroup(startRes, endRes, + startSeq, endSeq); + drawPanel(g1, startRes, endRes, startSeq, endSeq, 0); + ((Graphics2D) g1).setComposite( + AlphaComposite.getInstance(AlphaComposite.SRC_OVER)); + g1.drawImage(selectImage, 0, 0, this); + } - if (lcimg == null || imgWidth != lcimg.getWidth() - || imgHeight != lcimg.getHeight()) + /** + * Draw a wrapped alignment panel for printing + * + * @param g + * Graphics object to draw with + * @param canvasWidth + * width of drawing area + * @param canvasHeight + * height of drawing area + * @param startRes + * start residue of print area + */ + public void drawWrappedPanelForPrinting(Graphics g, int canvasWidth, + int canvasHeight, int startRes) + { + SequenceGroup group = av.getSelectionGroup(); + + drawWrappedPanel(g, canvasWidth, canvasHeight, startRes); + + if (group != null) { + BufferedImage selectImage = null; try { - lcimg = img = new BufferedImage(imgWidth, imgHeight, - BufferedImage.TYPE_INT_RGB); - gg = (Graphics2D) img.getGraphics(); - gg.setFont(av.getFont()); + selectImage = new BufferedImage(canvasWidth, canvasHeight, + BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works } catch (OutOfMemoryError er) { System.gc(); - System.err.println("SeqCanvas OutOfMemory Redraw Error.\n" + er); - new OOMWarning("Creating alignment image for display", er); - - return; + System.err.println("Print image OutOfMemory Error.\n" + er); + new OOMWarning("Creating wrapped alignment image for printing", er); + } + if (selectImage != null) + { + Graphics2D g2 = selectImage.createGraphics(); + setupSelectionGroup(g2, selectImage); + drawWrappedSelection(g2, group, canvasWidth, canvasHeight, + startRes); + + g2.setComposite( + AlphaComposite.getInstance(AlphaComposite.SRC_OVER)); + g.drawImage(selectImage, 0, 0, this); + g2.dispose(); } } + } - if (av.antiAlias) + /* + * Make a local image by combining the cached image img + * with any selection + */ + private BufferedImage buildLocalImage(BufferedImage selectImage) + { + // clone the cached image + BufferedImage lcimg = new BufferedImage(img.getWidth(), img.getHeight(), + img.getType()); + Graphics2D g2d = lcimg.createGraphics(); + g2d.drawImage(img, 0, 0, null); + + // overlay selection group on lcimg + if (selectImage != null) { - gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, - RenderingHints.VALUE_ANTIALIAS_ON); + g2d.setComposite( + AlphaComposite.getInstance(AlphaComposite.SRC_OVER)); + g2d.drawImage(selectImage, 0, 0, this); } + g2d.dispose(); - gg.setColor(Color.white); - gg.fillRect(0, 0, imgWidth, imgHeight); + return lcimg; + } - ViewportRanges ranges = av.getRanges(); - if (av.getWrapAlignment()) + /* + * Set up a buffered image of the correct height and size for the sequence canvas + */ + private BufferedImage setupImage() + { + BufferedImage lcimg = null; + + int width = getWidth(); + int height = getHeight(); + + width -= (width % charWidth); + height -= (height % charHeight); + + if ((width < 1) || (height < 1)) { - drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes()); + return null; } - else + + try { - drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(), - ranges.getStartSeq(), ranges.getEndSeq(), 0); - } + lcimg = new BufferedImage(width, height, + BufferedImage.TYPE_INT_ARGB); // ARGB so alpha compositing works + } catch (OutOfMemoryError er) + { + System.gc(); + System.err.println( + "Group image OutOfMemory Redraw Error.\n" + er); + new OOMWarning("Creating alignment image for display", er); - g.drawImage(lcimg, 0, 0, this); + return null; + } + return lcimg; } /** @@ -486,7 +617,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI * @param startRes * DOCUMENT ME! */ - public void drawWrappedPanel(Graphics g, int canvasWidth, + private void drawWrappedPanel(Graphics g, int canvasWidth, int canvasHeight, int startRes) { updateViewport(); @@ -625,7 +756,61 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } } - AnnotationPanel annotations; + /* + * Draw a selection group over a wrapped alignment + */ + private void drawWrappedSelection(Graphics2D g, SequenceGroup group, + int canvasWidth, + int canvasHeight, int startRes) + { + // height gap above each panel + int hgap = charHeight; + if (av.getScaleAboveWrapped()) + { + hgap += charHeight; + } + + int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / charWidth; + int cHeight = av.getAlignment().getHeight() * charHeight; + + int startx = startRes; + int endx; + int ypos = hgap; // vertical offset + int maxwidth = av.getAlignment().getWidth(); + + if (av.hasHiddenColumns()) + { + maxwidth = av.getAlignment().getHiddenColumns() + .findColumnPosition(maxwidth); + } + + // chop the wrapped alignment extent up into panel-sized blocks and treat + // each block as if it were a block from an unwrapped alignment + while ((ypos <= canvasHeight) && (startx < maxwidth)) + { + // set end value to be start + width, or maxwidth, whichever is smaller + endx = startx + cWidth - 1; + + if (endx > maxwidth) + { + endx = maxwidth; + } + + g.translate(LABEL_WEST, 0); + + drawUnwrappedSelection(g, group, startx, endx, 0, + av.getAlignment().getHeight() - 1, + ypos); + + g.translate(-LABEL_WEST, 0); + + // update vertical offset + ypos += cHeight + getAnnotationHeight() + hgap; + + // update horizontal offset + startx += cWidth; + } + } int getAnnotationHeight() { @@ -642,24 +827,24 @@ public class SeqCanvas extends JComponent implements ViewportListenerI return annotations.adjustPanelHeight(); } - /** - * DOCUMENT ME! + /* + * Draw an alignment panel for printing * * @param g1 - * DOCUMENT ME! + * Graphics object to draw with * @param startRes - * DOCUMENT ME! + * start residue of print area * @param endRes - * DOCUMENT ME! + * end residue of print area * @param startSeq - * DOCUMENT ME! + * start sequence of print area * @param endSeq - * DOCUMENT ME! + * end sequence of print area * @param offset - * DOCUMENT ME! + * vertical offset */ - public void drawPanel(Graphics g1, int startRes, int endRes, int startSeq, - int endSeq, int offset) + private void drawPanel(Graphics g1, int startRes, int endRes, + int startSeq, int endSeq, int offset) { updateViewport(); if (!av.hasHiddenColumns()) @@ -723,13 +908,11 @@ public class SeqCanvas extends JComponent implements ViewportListenerI } - // int startRes, int endRes, int startSeq, int endSeq, int x, int y, - // int x1, int x2, int y1, int y2, int startx, int starty, private void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq, int offset) { g.setFont(av.getFont()); - sr.prepare(g, av.isRenderGaps()); + seqRdr.prepare(g, av.isRenderGaps()); SequenceI nextSeq; @@ -744,7 +927,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI // empty continue; } - sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq), + seqRdr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq), startRes, endRes, offset + ((i - startSeq) * charHeight)); if (av.isShowSequenceFeatures()) @@ -763,10 +946,10 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { for (int r = 0; r < visibleResults.length; r += 2) { - sr.drawHighlightedText(nextSeq, visibleResults[r], - visibleResults[r + 1], - (visibleResults[r] - startRes) * charWidth, - offset + ((i - startSeq) * charHeight)); + seqRdr.drawHighlightedText(nextSeq, visibleResults[r], + visibleResults[r + 1], (visibleResults[r] - startRes) + * charWidth, offset + + ((i - startSeq) * charHeight)); } } } @@ -774,7 +957,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (av.cursorMode && cursorY == i && cursorX >= startRes && cursorX <= endRes) { - sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth, + seqRdr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth, offset + ((i - startSeq) * charHeight)); } } @@ -795,15 +978,11 @@ public class SeqCanvas extends JComponent implements ViewportListenerI // /////////////////////////////////// // Now outline any areas if necessary // /////////////////////////////////// - SequenceGroup group = av.getSelectionGroup(); - int sx = -1; - int sy = -1; - int ex = -1; + SequenceGroup group = null; int groupIndex = -1; - int visWidth = (endRes - startRes + 1) * charWidth; - if ((group == null) && (av.getAlignment().getGroups().size() > 0)) + if (av.getAlignment().getGroups().size() > 0) { group = av.getAlignment().getGroups().get(0); groupIndex = 0; @@ -811,168 +990,309 @@ public class SeqCanvas extends JComponent implements ViewportListenerI if (group != null) { + g.setStroke(new BasicStroke()); + g.setColor(group.getOutlineColour()); + do { - int oldY = -1; - int i = 0; - boolean inGroup = false; - int top = -1; - int bottom = -1; + drawPartialGroupOutline(g, group, startRes, endRes, startSeq, + endSeq, offset); + + groupIndex++; + + g.setStroke(new BasicStroke()); + + if (groupIndex >= av.getAlignment().getGroups().size()) + { + break; + } + + group = av.getAlignment().getGroups().get(groupIndex); + + } while (groupIndex < av.getAlignment().getGroups().size()); + + } + + } + + + /* + * Draw the selection group as a separate image and overlay + */ + private BufferedImage drawSelectionGroup(int startRes, int endRes, + int startSeq, int endSeq) + { + // get a new image of the correct size + BufferedImage selectionImage = setupImage(); + + if (selectionImage == null) + { + return null; + } + + SequenceGroup group = av.getSelectionGroup(); + if (group == null) + { + // nothing to draw + return null; + } + + // set up drawing colour + Graphics2D g = (Graphics2D) selectionImage.getGraphics(); + + setupSelectionGroup(g, selectionImage); + + if (!av.getWrapAlignment()) + { + drawUnwrappedSelection(g, group, startRes, endRes, startSeq, endSeq, + 0); + } + else + { + drawWrappedSelection(g, group, getWidth(), getHeight(), + av.getRanges().getStartRes()); + } + + g.dispose(); + return selectionImage; + } + + /* + * Set up graphics for selection group + */ + private void setupSelectionGroup(Graphics2D g, + BufferedImage selectionImage) + { + // set background to transparent + g.setComposite(AlphaComposite.getInstance(AlphaComposite.CLEAR, 0.0f)); + g.fillRect(0, 0, selectionImage.getWidth(), selectionImage.getHeight()); + + // set up foreground to draw red dashed line + g.setComposite(AlphaComposite.Src); + g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, + BasicStroke.JOIN_ROUND, 3f, new float[] + { 5f, 3f }, 0f)); + g.setColor(Color.RED); + } + + /* + * Draw a selection group over an unwrapped alignment + * @param g graphics object to draw with + * @param group selection group + * @param startRes start residue of area to draw + * @param endRes end residue of area to draw + * @param startSeq start sequence of area to draw + * @param endSeq end sequence of area to draw + * @param offset vertical offset (used when called from wrapped alignment code) + */ + private void drawUnwrappedSelection(Graphics2D g, SequenceGroup group, + int startRes, int endRes, int startSeq, int endSeq, int offset) + { + if (!av.hasHiddenColumns()) + { + drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq, + offset); + } + else + { + // package into blocks of visible columns + int screenY = 0; + int blockStart = startRes; + int blockEnd = endRes; + + for (int[] region : av.getAlignment().getHiddenColumns() + .getHiddenColumnsCopy()) + { + int hideStart = region[0]; + int hideEnd = region[1]; - for (i = startSeq; i <= endSeq; i++) + if (hideStart <= blockStart) { - sx = (group.getStartRes() - startRes) * charWidth; - sy = offset + ((i - startSeq) * charHeight); - ex = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth) - - 1; + blockStart += (hideEnd - hideStart) + 1; + continue; + } - if (sx + ex < 0 || sx > visWidth) - { - continue; - } + blockEnd = hideStart - 1; - if ((sx <= (endRes - startRes) * charWidth) - && group.getSequences(null) - .contains(av.getAlignment().getSequenceAt(i))) - { - if ((bottom == -1) && !group.getSequences(null) - .contains(av.getAlignment().getSequenceAt(i + 1))) - { - bottom = sy + charHeight; - } - - if (!inGroup) - { - if (((top == -1) && (i == 0)) || !group.getSequences(null) - .contains(av.getAlignment().getSequenceAt(i - 1))) - { - top = sy; - } - - oldY = sy; - inGroup = true; - - if (group == av.getSelectionGroup()) - { - g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT, - BasicStroke.JOIN_ROUND, 3f, new float[] - { 5f, 3f }, 0f)); - g.setColor(Color.RED); - } - else - { - g.setStroke(new BasicStroke()); - g.setColor(group.getOutlineColour()); - } - } - } - else + g.translate(screenY * charWidth, 0); + drawPartialGroupOutline(g, group, + blockStart, blockEnd, startSeq, endSeq, offset); + + g.translate(-screenY * charWidth, 0); + screenY += blockEnd - blockStart + 1; + blockStart = hideEnd + 1; + + if (screenY > (endRes - startRes)) + { + // already rendered last block + break; + } + } + + if (screenY <= (endRes - startRes)) + { + // remaining visible region to render + blockEnd = blockStart + (endRes - startRes) - screenY; + g.translate(screenY * charWidth, 0); + drawPartialGroupOutline(g, group, + blockStart, blockEnd, startSeq, endSeq, offset); + + g.translate(-screenY * charWidth, 0); + } + } + } + + /* + * Draw the selection group as a separate image and overlay + */ + private void drawPartialGroupOutline(Graphics2D g, SequenceGroup group, + int startRes, int endRes, int startSeq, int endSeq, + int verticalOffset) + { + int visWidth = (endRes - startRes + 1) * charWidth; + + int oldY = -1; + int i = 0; + boolean inGroup = false; + int top = -1; + int bottom = -1; + + int sx = -1; + int sy = -1; + int xwidth = -1; + + for (i = startSeq; i <= endSeq; i++) + { + // position of start residue of group relative to startRes, in pixels + sx = (group.getStartRes() - startRes) * charWidth; + + // width of group in pixels + xwidth = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth) + - 1; + + sy = verticalOffset + (i - startSeq) * charHeight; + + if (sx + xwidth < 0 || sx > visWidth) + { + continue; + } + + if ((sx <= (endRes - startRes) * charWidth) + && group.getSequences(null) + .contains(av.getAlignment().getSequenceAt(i))) + { + if ((bottom == -1) && !group.getSequences(null) + .contains(av.getAlignment().getSequenceAt(i + 1))) + { + bottom = sy + charHeight; + } + + if (!inGroup) + { + if (((top == -1) && (i == 0)) || !group.getSequences(null) + .contains(av.getAlignment().getSequenceAt(i - 1))) { - if (inGroup) - { - if (sx >= 0 && sx < visWidth) - { - g.drawLine(sx, oldY, sx, sy); - } - - if (sx + ex < visWidth) - { - g.drawLine(sx + ex, oldY, sx + ex, sy); - } - - if (sx < 0) - { - ex += sx; - sx = 0; - } - - if (sx + ex > visWidth) - { - ex = visWidth; - } - - else if (sx + ex >= (endRes - startRes + 1) * charWidth) - { - ex = (endRes - startRes + 1) * charWidth; - } - - if (top != -1) - { - g.drawLine(sx, top, sx + ex, top); - top = -1; - } - - if (bottom != -1) - { - g.drawLine(sx, bottom, sx + ex, bottom); - bottom = -1; - } - - inGroup = false; - } + top = sy; } - } + oldY = sy; + inGroup = true; + } + } + else + { if (inGroup) { - sy = offset + ((i - startSeq) * charHeight); + // if start position is visible, draw vertical line to left of + // group if (sx >= 0 && sx < visWidth) { g.drawLine(sx, oldY, sx, sy); } - if (sx + ex < visWidth) + // if end position is visible, draw vertical line to right of + // group + if (sx + xwidth < visWidth) { - g.drawLine(sx + ex, oldY, sx + ex, sy); + g.drawLine(sx + xwidth, oldY, sx + xwidth, sy); } if (sx < 0) { - ex += sx; + xwidth += sx; sx = 0; } - if (sx + ex > visWidth) + // don't let width extend beyond current block, or group extent + // fixes JAL-2672 + if (sx + xwidth >= (endRes - startRes + 1) * charWidth) { - ex = visWidth; + xwidth = (endRes - startRes + 1) * charWidth - sx; } - else if (sx + ex >= (endRes - startRes + 1) * charWidth) - { - ex = (endRes - startRes + 1) * charWidth; - } - + + // draw horizontal line at top of group if (top != -1) { - g.drawLine(sx, top, sx + ex, top); + g.drawLine(sx, top, sx + xwidth, top); top = -1; } + // draw horizontal line at bottom of group if (bottom != -1) { - g.drawLine(sx, bottom - 1, sx + ex, bottom - 1); + g.drawLine(sx, bottom, sx + xwidth, bottom); bottom = -1; } inGroup = false; } + } + } - groupIndex++; + if (inGroup) + { + sy = verticalOffset + ((i - startSeq) * charHeight); + if (sx >= 0 && sx < visWidth) + { + g.drawLine(sx, oldY, sx, sy); + } - g.setStroke(new BasicStroke()); + if (sx + xwidth < visWidth) + { + g.drawLine(sx + xwidth, oldY, sx + xwidth, sy); + } - if (groupIndex >= av.getAlignment().getGroups().size()) - { - break; - } + if (sx < 0) + { + xwidth += sx; + sx = 0; + } - group = av.getAlignment().getGroups().get(groupIndex); + if (sx + xwidth > visWidth) + { + xwidth = visWidth; + } + else if (sx + xwidth >= (endRes - startRes + 1) * charWidth) + { + xwidth = (endRes - startRes + 1) * charWidth; + } - } while (groupIndex < av.getAlignment().getGroups().size()); + if (top != -1) + { + g.drawLine(sx, top, sx + xwidth, top); + top = -1; + } - } + if (bottom != -1) + { + g.drawLine(sx, bottom - 1, sx + xwidth, bottom - 1); + bottom = -1; + } + inGroup = false; + } } - + /** * DOCUMENT ME! * @@ -993,7 +1313,12 @@ public class SeqCanvas extends JComponent implements ViewportListenerI { String eventName = evt.getPropertyName(); - if (av.getWrapAlignment()) + if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED)) + { + fastPaint = true; + repaint(); + } + else if (av.getWrapAlignment()) { if (eventName.equals(ViewportRanges.STARTRES)) { diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 056a602..c3aa15f 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1095,7 +1095,7 @@ public class SeqPanel extends JPanel } mouseDragging = true; - if (scrollThread != null) + if ((scrollThread != null) && (scrollThread.isRunning())) { scrollThread.setEvent(evt); } @@ -1521,9 +1521,9 @@ public class SeqPanel extends JPanel oldSeq = 0; } - if (scrollThread != null) + if ((scrollThread != null) && (scrollThread.isRunning())) { - scrollThread.running = false; + scrollThread.stopScrolling(); scrollThread = null; } } @@ -1542,7 +1542,7 @@ public class SeqPanel extends JPanel return; } - if (mouseDragging) + if (mouseDragging && scrollThread == null) { scrollThread = new ScrollThread(); } @@ -1710,43 +1710,53 @@ public class SeqPanel extends JPanel if (stretchGroup == null) { - // Only if left mouse button do we want to change group sizes + createStretchGroup(res, sequence); + } - // define a new group here - SequenceGroup sg = new SequenceGroup(); - sg.setStartRes(res); - sg.setEndRes(res); - sg.addSequence(sequence, false); - av.setSelectionGroup(sg); - stretchGroup = sg; + if (stretchGroup != null) + { + stretchGroup.addPropertyChangeListener(seqCanvas); + } - if (av.getConservationSelected()) - { - SliderPanel.setConservationSlider(ap, av.getResidueShading(), - ap.getViewName()); - } + seqCanvas.repaint(); + } - if (av.getAbovePIDThreshold()) - { - SliderPanel.setPIDSliderSource(ap, av.getResidueShading(), - ap.getViewName()); - } - // TODO: stretchGroup will always be not null. Is this a merge error ? - if ((stretchGroup != null) && (stretchGroup.getEndRes() == res)) - { - // Edit end res position of selected group - changeEndRes = true; - } - else if ((stretchGroup != null) - && (stretchGroup.getStartRes() == res)) - { - // Edit end res position of selected group - changeStartRes = true; - } - stretchGroup.getWidth(); + private void createStretchGroup(int res, SequenceI sequence) + { + // Only if left mouse button do we want to change group sizes + // define a new group here + SequenceGroup sg = new SequenceGroup(); + sg.setStartRes(res); + sg.setEndRes(res); + sg.addSequence(sequence, false); + av.setSelectionGroup(sg); + stretchGroup = sg; + + if (av.getConservationSelected()) + { + SliderPanel.setConservationSlider(ap, av.getResidueShading(), + ap.getViewName()); } - seqCanvas.repaint(); + if (av.getAbovePIDThreshold()) + { + SliderPanel.setPIDSliderSource(ap, av.getResidueShading(), + ap.getViewName()); + } + // TODO: stretchGroup will always be not null. Is this a merge error ? + // or is there a threading issue here? + if ((stretchGroup != null) && (stretchGroup.getEndRes() == res)) + { + // Edit end res position of selected group + changeEndRes = true; + } + else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res)) + { + // Edit end res position of selected group + changeStartRes = true; + } + stretchGroup.getWidth(); + } /** @@ -1795,6 +1805,9 @@ public class SeqPanel extends JPanel { return; } + + stretchGroup.removePropertyChangeListener(seqCanvas); + // always do this - annotation has own state // but defer colourscheme update until hidden sequences are passed in boolean vischange = stretchGroup.recalcConservation(true); @@ -1936,21 +1949,19 @@ public class SeqPanel extends JPanel mouseDragging = true; - if (scrollThread != null) + if ((scrollThread != null) && (scrollThread.isRunning())) { scrollThread.setEvent(evt); } - - seqCanvas.repaint(); } void scrollCanvas(MouseEvent evt) { if (evt == null) { - if (scrollThread != null) + if ((scrollThread != null) && (scrollThread.isRunning())) { - scrollThread.running = false; + scrollThread.stopScrolling(); scrollThread = null; } mouseDragging = false; @@ -1973,7 +1984,7 @@ public class SeqPanel extends JPanel { MouseEvent evt; - boolean running = false; + private volatile boolean threadRunning = true; public ScrollThread() { @@ -1987,37 +1998,40 @@ public class SeqPanel extends JPanel public void stopScrolling() { - running = false; + threadRunning = false; + } + + public boolean isRunning() + { + return threadRunning; } @Override public void run() { - running = true; - - while (running) + while (threadRunning) { if (evt != null) { if (mouseDragging && (evt.getY() < 0) && (av.getRanges().getStartSeq() > 0)) { - running = av.getRanges().scrollUp(true); + av.getRanges().scrollUp(true); } if (mouseDragging && (evt.getY() >= getHeight()) && (av .getAlignment().getHeight() > av.getRanges().getEndSeq())) { - running = av.getRanges().scrollUp(false); + av.getRanges().scrollUp(false); } if (mouseDragging && (evt.getX() < 0)) { - running = av.getRanges().scrollRight(false); + av.getRanges().scrollRight(false); } else if (mouseDragging && (evt.getX() >= getWidth())) { - running = av.getRanges().scrollRight(true); + av.getRanges().scrollRight(true); } } diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java index 4498f88..5be7f55 100755 --- a/src/jalview/gui/SequenceRenderer.java +++ b/src/jalview/gui/SequenceRenderer.java @@ -23,9 +23,8 @@ package jalview.gui; import jalview.api.AlignViewportI; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; -import jalview.renderer.ResidueShaderI; +import jalview.renderer.ResidueColourFinder; import jalview.renderer.seqfeatures.FeatureColourFinder; -import jalview.util.Comparison; import java.awt.Color; import java.awt.FontMetrics; @@ -41,17 +40,15 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer boolean renderGaps = true; - SequenceGroup currentSequenceGroup = null; - SequenceGroup[] allGroups = null; - Color resBoxColour; + // Color resBoxColour; Graphics graphics; boolean monospacedFont; - boolean forOverview = false; + ResidueColourFinder resColourFinder; /** * Creates a new SequenceRenderer object @@ -61,6 +58,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer public SequenceRenderer(AlignViewportI viewport) { this.av = viewport; + resColourFinder = new ResidueColourFinder(); } /** @@ -83,26 +81,6 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer this.renderGaps = renderGaps; } - protected Color getResidueBoxColour(SequenceI seq, int i) - { - // rate limiting step when rendering overview for lots of groups - allGroups = av.getAlignment().findAllGroups(seq); - - if (inCurrentSequenceGroup(i)) - { - if (currentSequenceGroup.getDisplayBoxes()) - { - getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, i); - } - } - else if (av.getShowBoxes()) - { - getBoxColour(av.getResidueShading(), seq, i); - } - - return resBoxColour; - } - /** * Get the residue colour at the given sequence position - as determined by * the sequence group colour (if any), else the colour scheme, possibly @@ -117,39 +95,10 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer public Color getResidueColour(final SequenceI seq, int position, FeatureColourFinder finder) { - Color col = getResidueBoxColour(seq, position); - - if (finder != null) - { - col = finder.findFeatureColour(col, seq, position); - } - return col; - } - - /** - * DOCUMENT ME! - * - * @param shader - * DOCUMENT ME! - * @param seq - * DOCUMENT ME! - * @param i - * DOCUMENT ME! - */ - void getBoxColour(ResidueShaderI shader, SequenceI seq, int i) - { - if (shader.getColourScheme() != null) - { - resBoxColour = shader.findColour(seq.getCharAt(i), i, seq); - } - else if (forOverview && !Comparison.isGap(seq.getCharAt(i))) - { - resBoxColour = Color.lightGray; - } - else - { - resBoxColour = Color.white; - } + return resColourFinder.getResidueColour(av.getShowBoxes(), + av.getResidueShading(), + allGroups, seq, position, + finder); } /** @@ -208,6 +157,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer public synchronized void drawBoxes(SequenceI seq, int start, int end, int y1) { + Color resBoxColour = Color.white; + if (seq == null) { return; // fix for racecondition @@ -227,17 +178,22 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer if (i < length) { - if (inCurrentSequenceGroup(i)) + SequenceGroup currentSequenceGroup = resColourFinder + .getCurrentSequenceGroup( + allGroups, i); + if (currentSequenceGroup != null) { if (currentSequenceGroup.getDisplayBoxes()) { - getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, + resBoxColour = resColourFinder.getBoxColour( + currentSequenceGroup.getGroupColourScheme(), seq, i); } } else if (av.getShowBoxes()) { - getBoxColour(av.getResidueShading(), seq, i); + resBoxColour = resColourFinder + .getBoxColour(av.getResidueShading(), seq, i); } } @@ -317,10 +273,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer boolean srep = av.isDisplayReferenceSeq(); boolean getboxColour = false; boolean isarep = av.getAlignment().getSeqrep() == seq; - boolean isgrep = currentSequenceGroup != null - ? currentSequenceGroup.getSeqrep() == seq - : false; - char sr_c; + Color resBoxColour = Color.white; + for (int i = start; i <= end; i++) { @@ -333,7 +287,10 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer continue; } - if (inCurrentSequenceGroup(i)) + SequenceGroup currentSequenceGroup = resColourFinder + .getCurrentSequenceGroup( + allGroups, i); + if (currentSequenceGroup != null) { if (!currentSequenceGroup.getDisplayText()) { @@ -344,7 +301,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer || currentSequenceGroup.getColourText()) { getboxColour = true; - getBoxColour(currentSequenceGroup.getGroupColourScheme(), seq, + resBoxColour = resColourFinder.getBoxColour( + currentSequenceGroup.getGroupColourScheme(), seq, i); if (currentSequenceGroup.getColourText()) @@ -366,6 +324,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer { graphics.setColor(currentSequenceGroup.textColour); } + boolean isgrep = currentSequenceGroup != null + ? currentSequenceGroup.getSeqrep() == seq : false; if (!isarep && !isgrep && currentSequenceGroup.getShowNonconserved()) // todo // optimize @@ -386,7 +346,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer if (av.getColourText()) { getboxColour = true; - getBoxColour(av.getResidueShading(), seq, i); + resBoxColour = resColourFinder + .getBoxColour(av.getResidueShading(), seq, i); if (av.getShowBoxes()) { @@ -402,7 +363,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer { if (!getboxColour) { - getBoxColour(av.getResidueShading(), seq, i); + resBoxColour = resColourFinder + .getBoxColour(av.getResidueShading(), seq, i); } if (resBoxColour.getRed() + resBoxColour.getBlue() @@ -473,35 +435,6 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer /** * DOCUMENT ME! * - * @param res - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - boolean inCurrentSequenceGroup(int res) - { - if (allGroups == null) - { - return false; - } - - for (int i = 0; i < allGroups.length; i++) - { - if ((allGroups[i].getStartRes() <= res) - && (allGroups[i].getEndRes() >= res)) - { - currentSequenceGroup = allGroups[i]; - - return true; - } - } - - return false; - } - - /** - * DOCUMENT ME! - * * @param seq * DOCUMENT ME! * @param start diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index 633d2b8..1ca0802 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -95,11 +95,11 @@ public class GPreferences extends JPanel protected JCheckBox rightAlign = new JCheckBox(); - protected JComboBox fontSizeCB = new JComboBox(); + protected JComboBox fontSizeCB = new JComboBox<>(); - protected JComboBox fontStyleCB = new JComboBox(); + protected JComboBox fontStyleCB = new JComboBox<>(); - protected JComboBox fontNameCB = new JComboBox(); + protected JComboBox fontNameCB = new JComboBox<>(); protected JCheckBox showOccupancy = new JCheckBox(); @@ -111,15 +111,15 @@ public class GPreferences extends JPanel protected JCheckBox scaleProteinToCdna = new JCheckBox(); - protected JComboBox gapSymbolCB = new JComboBox(); + protected JComboBox gapSymbolCB = new JComboBox<>(); protected JCheckBox wrap = new JCheckBox(); - protected JComboBox sortby = new JComboBox(); + protected JComboBox sortby = new JComboBox<>(); - protected JComboBox sortAnnBy = new JComboBox(); + protected JComboBox sortAnnBy = new JComboBox<>(); - protected JComboBox sortAutocalc = new JComboBox(); + protected JComboBox sortAutocalc = new JComboBox<>(); protected JCheckBox startupCheckbox = new JCheckBox(); @@ -159,7 +159,7 @@ public class GPreferences extends JPanel protected JCheckBox addTempFactor = new JCheckBox(); - protected JComboBox structViewer = new JComboBox(); + protected JComboBox structViewer = new JComboBox<>(); protected JTextField chimeraPath = new JTextField(); @@ -176,9 +176,22 @@ public class GPreferences extends JPanel protected JPanel maxColour = new JPanel(); - protected JComboBox protColour = new JComboBox(); + protected JComboBox protColour = new JComboBox<>(); - protected JComboBox nucColour = new JComboBox(); + protected JComboBox nucColour = new JComboBox<>(); + + /* + * Overview tab components + */ + protected JPanel gapColour = new JPanel(); + + protected JPanel hiddenColour = new JPanel(); + + protected JCheckBox useLegacyGap; + + protected JCheckBox showHiddenAtStart; + + protected JLabel gapLabel; /* * Connections tab components @@ -216,7 +229,7 @@ public class GPreferences extends JPanel /* * Output tab components */ - protected JComboBox